TRANSFAC® is a unique knowledge-base containing published data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes. The extensive compilation of binding sites provides the most comprehensive data set of transcription factor – gene interactions available. The same data also forms the basis of derived positional weight matrices which can be used with the included Match™ tool to search DNA sequences for putative transcription factor binding sites – a method that is crucial for filling in gaps in the published literature. Integrated transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project complement the curated and predicted binding site data. All data, including the transcription factor – gene interactions, matrix library and command line Match™ program are available for download, for easy integration into your own or third party tools.

Use the newly integrated F-Match algorithm to perform comparative promoter analysis of high-throughput microarray data, identifying the transcription factors most likely to have induced the experimentally observed pattern of gene expression. Or use the integrated DECOD algorithm to identify novel, as-yet-uncharacterized motifs within ChIP-Seq or other data. All algorithms work with the built in promoter library for human, mouse and rat as well as multiple plant species including A. thaliana, O. sativa, and G. max or your own submitted sequences.

Model how transcription factors act together to affect gene expression patterns observed in microarray and RNA-Seq experiments in order to understand the cause, not just the effect, of differential expression in response to drug treatment, disease state, environmental conditions, and more

Integrate TRANSFAC®’s positional weight matrices into your own or 3rd party tools with the flat file download option

DownloadA download subscription provides access to flat files containing data for factors, matrices, binding sites, genes, ChIP fragments and other supporting information, as well as command line access to the Match tool. In this way, TRANSFAC data and positional weight matrices may be integrated into your own, or 3rd party, analysis pipelines and tools. However redistribution of, or public access to / display of, the data or results generated by TRANSFAC positional weight matrices is not allowed without prior written consent. Users interested in using TRANSFAC®’s Match tool for prediction of transcription factor binding sites within CLCbio’s Genomics Workbench software must purchase the TRANSFAC TFBS plugin or a TRANSFAC® download subscription. A download subscription does not provide access to the TRANSFAC web interface.

Relational Database DownloadA relational database download subscription allows for local installation of the complete TRANSFAC relational database. A local installation allows you to query and extract all fields of TRANSFAC data (including transcription factor disease associations and transcription factor organ/tissue/cell/tumor expression patterns) for integration into your own, or 3rd party, analysis pipelines and tools. However redistribution of, or public access to / display of, the data is not allowed without prior written consent. Relational database download subscriptions do not provide access to the TRANSFAC web interface. MySQL platform is supported.

Click here for a table comparison of features available in online vs. download options.